A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/home/moji-lin/rna-seq-reanalysis/data/processed
General Statistics
| Sample Name | Error rate | Non-primary | Reads mapped | % Mapped | % Proper pairs | % MapQ 0 reads | Total seqs | Mean insert | Reads | Reads mapped | % Reads mapped | % Aligned | M Aligned | Library types | CFR | M Bias | % Aligned |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| processed | Bam_related_logs | logs_trimmed_KO_SRR13633857 | trimmed_KO_SRR13633857 | 0.15% | 5.6M | 26.8M | 98.3% | 0.0% | 0.3% | 27.3M | 0.0bp | 32.9M | 32.4M | 98.6% | 98.3% | |||||
| processed | Bam_related_logs | logs_trimmed_KO_SRR13633858 | trimmed_KO_SRR13633858 | 0.15% | 5.6M | 26.7M | 98.1% | 0.0% | 0.4% | 27.2M | 0.0bp | 32.9M | 32.4M | 98.4% | 98.1% | |||||
| processed | Bam_related_logs | logs_trimmed_KO_SRR13633859 | trimmed_KO_SRR13633859 | 0.15% | 5.5M | 27.0M | 98.4% | 0.0% | 0.4% | 27.4M | 0.0bp | 32.9M | 32.4M | 98.7% | 98.4% | |||||
| processed | Bam_related_logs | logs_trimmed_KO_SRR13633860 | trimmed_KO_SRR13633860 | 0.15% | 5.4M | 26.9M | 98.4% | 0.0% | 0.4% | 27.4M | 0.0bp | 32.8M | 32.4M | 98.7% | 98.4% | |||||
| processed | Bam_related_logs | logs_trimmed_WT_SRR13633855 | trimmed_WT_SRR13633855 | 0.14% | 6.2M | 27.0M | 98.5% | 0.0% | 0.4% | 27.4M | 0.0bp | 33.6M | 33.2M | 98.7% | 98.5% | |||||
| processed | Bam_related_logs | logs_trimmed_WT_SRR13633856 | trimmed_WT_SRR13633856 | 0.15% | 6.7M | 27.0M | 98.4% | 0.0% | 0.4% | 27.4M | 0.0bp | 34.1M | 33.7M | 98.7% | 98.4% | |||||
| processed | quant_results | trimmed_KO_SRR13633857 | trimmed_KO_SRR13633857 | 100.0% | 0.5 | |||||||||||||||
| processed | quant_results | trimmed_KO_SRR13633858 | trimmed_KO_SRR13633858 | 100.0% | 0.5 | |||||||||||||||
| processed | quant_results | trimmed_KO_SRR13633859 | trimmed_KO_SRR13633859 | 100.0% | 0.5 | |||||||||||||||
| processed | quant_results | trimmed_KO_SRR13633860 | trimmed_KO_SRR13633860 | 100.0% | 0.5 | |||||||||||||||
| processed | quant_results | trimmed_WT_SRR13633855 | trimmed_WT_SRR13633855 | 100.0% | 0.5 | |||||||||||||||
| processed | quant_results | trimmed_WT_SRR13633856 | trimmed_WT_SRR13633856 | 100.0% | 0.5 | |||||||||||||||
| quant_results | trimmed_KO_SRR13633857 | aux_info | trimmed_KO_SRR13633857 | 94.5% | 25.8M | U | ||||||||||||||
| quant_results | trimmed_KO_SRR13633858 | aux_info | trimmed_KO_SRR13633858 | 93.8% | 25.6M | U | ||||||||||||||
| quant_results | trimmed_KO_SRR13633859 | aux_info | trimmed_KO_SRR13633859 | 94.3% | 25.8M | U | ||||||||||||||
| quant_results | trimmed_KO_SRR13633860 | aux_info | trimmed_KO_SRR13633860 | 93.9% | 25.7M | U | ||||||||||||||
| quant_results | trimmed_WT_SRR13633855 | aux_info | trimmed_WT_SRR13633855 | 94.5% | 25.9M | U | ||||||||||||||
| quant_results | trimmed_WT_SRR13633856 | aux_info | trimmed_WT_SRR13633856 | 93.0% | 25.5M | U |
Samtools
1.19.2
HTSlib:
1.19
Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352
Percent mapped
Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.
For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.
Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).
Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.
Alignment stats
This module parses the output from samtools stats. All numbers in millions.
Flagstat
This module parses the output from samtools flagstat
Flagstat: Percentage of total
This module parses the output from samtools flagstat
Salmon
1.10.3
Quantifies expression of transcripts using RNA-seq data.URL: https://combine-lab.github.io/salmonDOI: 10.1038/nmeth.4197
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Single-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 3 possible types of alignment:
- SE mapped uniquely: Read has only one occurence in the reference genome.
- SE multimapped: Read has multiple occurence.
- SE not aligned: Read has no occurence.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| Salmon | Salmon | 1.10.3 |
| Samtools | HTSlib | 1.19 |
| Samtools | 1.19.2 |